Coral reef ecosystems play a vital role in sustaining the health of oceanic life and the livelihoods of coastal population. Despite their importance, these reefs face severe threats from climate change, pollution, and human activities. Hence, continuous monitoring of coral reefs around the world has become a vital research to address reef health, reef restoration, reef resources, reef services, and coastal livelihood. Existing reef monitoring methods are limited in their capacity to deliver cost-effective, noninvasive, and objective evaluations of coral reef structure and complexity and fail to provide a permanent record of reef images, making photogrammetry a more effective alternative. This is the first ever study to employ 3D photogrammetry method and establish the baseline 3D photogrammetry-based coral reef maps in India. By establishing permanent monitoring stations and utilizing advanced photogrammetry, this study aims to provide a comprehensive assessment of the coral cover status, reef structure, and complexity of coral reefs at Grand Island, Goa, and Palk Bay, Tamil Nadu. A detailed transect mosaic reconstructions were generated through in situ underwater photogrammetry to evaluate coral cover, health indicators, and substrate composition. In the Grande Island region, Navy Bay and Shelter Cove were surveyed, revealing Turbinaria sp. as a dominant coral with a total live coral cover of 41.16 ± 18.77%. Dead coral with algae (DCA) represents 13.3 ± 5.77% of the surveyed area. Significantly, the coral killing invasive encrusting sponge, Cliona, impacting Turbinaria sp. and Favites sp. was observed. Coral substrate was primarily composed of sand, gravel, and coral rubble, covering 44.65 ± 14.33% of the transects. In the Palk Bay region, surveys were conducted at Mandapam Camp and Rameswaram, where Acropora sp. emerged as the dominant coral genus, with a total live coral cover of 32.17 ± 13.86%. However, the reef ecosystem in Palk Bay is evidently under degradation, with apparent evidences of broken and dead fragments of Acropora sp. constituting a major component of the reef substrate (64.27 ± 7.03%). This degradation is likely attributed to heavy boat traffic and fishing, which has caused extensive fragmentation of the coral colonies. Additionally, the infestation of Serpulidae worms and prevalence of pink spot on Porites sp. represented 2.02% cover of one transect. Coral-infesting sponges were also observed, with diseased and infected corals covering 0.6 ± 0.05% of the surveyed area. The anthropogenic impact in Palk Bay was more pronounced than in Grande Island, as evidenced by toppled Acropora sp. colonies, likely caused by boat anchor dragging, and the alarming discovery of plastic cement bags covering coral colonies. These bags smother and weaken corals, promoting the growth of turf algae and sponges, further compromising reef health. The absence of reef-associated fishes across survey sites highlights the severe impact of overfishing and other human activities. Compared to the relatively well-maintained reefs of Grande Island, the proximity of Palk Bay to the shore has exacerbated the degradation. Continued long-term monitoring of Indian reefs is in progress, aiming to develop a permanent repository of photo mosaics that will provide a valuable baseline dataset for future studies and research endeavors. The findings from this assessment underscore the urgent need for ongoing monitoring, expanded surveys, and targeted conservation efforts to mitigate further damage and restore the health of coral reef ecosystems in these regions.